Engineering a model protein cavity to catalyze the Kemp elimination (Q27673337)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

title

Engineering a model protein cavity to catalyze the Kemp elimination (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

author name string

Brian K Shoichet

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

language of work or name

English

0 references

publication date

17 September 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

Proceedings of the National Academy of Sciences of the United States of America

13 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

volume

109

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

issue

40

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

page(s)

16179-16183

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

13 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Iterative approach to computational enzyme design

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Design of a switchable eliminase

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Lessons from the lysozyme of phage T4

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Structural Bases for Stability–Function Tradeoffs in Antibiotic Resistance

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Following evolutionary paths to protein-protein interactions with high affinity and selectivity

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Use of stabilizing mutations to engineer a charged group within a ligand-binding hydrophobic cavity in T4 lysozyme

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Kemp elimination catalysts by computational enzyme design

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Exploring subdomain cooperativity in T4 lysozyme I: Structural and energetic studies of a circular permutant and protein fragment

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

A model binding site for testing scoring functions in molecular docking

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Structural bases of stability-function tradeoffs in enzymes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Evolution of an antibiotic resistance enzyme constrained by stability and activity trade-offs

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

A relationship between protein stability and protein function

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

An exciting but challenging road ahead for computational enzyme design

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Large shifts in pKa values of lysine residues buried inside a protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Optimizing non-natural protein function with directed evolution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Origins of catalysis by computationally designed retroaldolase enzymes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Stability effects of mutations and protein evolvability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

How protein stability and new functions trade off

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Structural origins of efficient proton abstraction from carbon by a catalytic antibody

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Energetics of enzyme catalysis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

New algorithms and an in silico benchmark for computational enzyme design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Evaluation of catalytic free energies in genetically modified proteins

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm

2 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1208076109

Computational protein design promises to revolutionize protein engineering

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1208076109

Large rate accelerations in antibody catalysis by strategic use of haptenic charge

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1208076109

Off-the-shelf proteins that rival tailor-made antibodies as catalysts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1208076109

Stability and function: two constraints in the evolution of barstar and other proteins

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3479533

Buffers of constant ionic strength for studying pH-dependent processes

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22988064

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1208076109

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22988064%20AND%20SRC:MED&resulttype=core&format=json